# cat /etc/apache2/ports.conf
# If you just change the port or add more ports here, you will likely also
# have to change the VirtualHost statement in
# /etc/apache2/sites-enabled/000-default
# This is also true if you have upgraded from before 2.2.9-3 (i.e. from
# Debian etch). See /usr/share/doc/apache2.2-common/NEWS.Debian.gz and
# README.Debian.gz

NameVirtualHost *:80
Listen 80

<IfModule mod_ssl.c>
# If you add NameVirtualHost *:443 here, you will also have to change
# the VirtualHost statement in /etc/apache2/sites-available/default-ssl
# to <VirtualHost *:443>
# Server Name Indication for SSL named virtual hosts is currently not
# supported by MSIE on Windows XP.
Listen 443
</IfModule>

I have the same symptom, my system runs on debian squeeze. Altough all sites appear to work fine this warning message is annoying... could we somehow get rid off it like it wasn't there in the earlier versions...

Upon Upgrading to 3.0.5.2 in a multi-server setup
what is the correct selection in Reconfigure Permissions in master database? (yes,no) [no]:

Don't understand the semantics, your website says:

If this is a slave server in a multiserver setup, then choose “yes” here on at least one of the slave servers. For single server installations, choose ‘no’. Then you were asked if the services shall be reconfigured:

Thats ok and not a error. The message means that you can add hosts with * instead of a IP on you server. So its not a issue, apache notices you just about the possibility that banevirtualhosts with * on these two orts are available but not in use yet.